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labgem / PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes
https://ppanggolin.readthedocs.io
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TypeError: Population must be a sequence. For dicts or sets, use sorted(d). #293

Open ericolo opened 2 weeks ago

ericolo commented 2 weeks ago

Hi !

I get this error and I can't debug why it happens, the input files look good to me

TypeError: Population must be a sequence. For dicts or sets, use sorted(d).

I'm using ppanggolin like this: ppanggolin workflow --anno list_genomes.tsv -c 64 -o output --clusters clusters.tsv --infer_singletons --rarefaction

Thanks in advance ! Eric

axbazin commented 2 weeks ago

Hi !

Any chance you could provide the complete log? It's nearly impossible to identify the location of the problem without the full trace (which should be in the log file where this error is written) with something as generic as this kind of error.

Adelme

ericolo commented 2 weeks ago

Hello,

Sorry for the very little info, this is the log file obtained on that run: debug_log.txt

And here is the complete error message: error.txt

Thanks !

axbazin commented 2 weeks ago

I see, thanks a lot !

This is definitely a bug, and I think it's related to having exactly the number of genomes that you have in your run here (501?). In the meantime, until we resolve this, I believe that increasing the chunk_size in the "partition" step might fix this error.

ericolo commented 1 week ago

Indeed if I remove one genome from the list it works fine, haven't tried the chunk_size yet.